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- PDB-1upd: Oxidized STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURIC... -

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Basic information

Entry
Database: PDB / ID: 1upd
TitleOxidized STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / TETRAHEME CYTOCHROME C
Function / homology
Function and homology information


electron transfer activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Class III cytochrome C family protein
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å
AuthorsBento, I. / Matias, P.M. / Baptista, A.M. / Da Costa, P.N. / Van Dongen, W.M.A.M. / Saraiva, L.M. / Schneider, T.R. / Soares, C.M. / Carrondo, M.A.
Citation
Journal: Proteins / Year: 2004
Title: Molecular Basis for Redox-Bohr and Cooperative Effects in Cytochrome C3 from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies of Oxidized and Reduced High- ...Title: Molecular Basis for Redox-Bohr and Cooperative Effects in Cytochrome C3 from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies of Oxidized and Reduced High-Resolution Structures at Ph 7.6
Authors: Bento, I. / Matias, P.M. / Baptista, A.M. / Da Costa, P.N. / Van Dongen, W.M.A.M. / Saraiva, L.M. / Schneider, T.R. / Soares, C.M. / Carrondo, M.A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome
Authors: Louro, R.O. / Bento, I. / Matias, P.M. / Catarino, T. / Baptista, A.M. / Soares, C.M. / Carrondo, M.A. / Turner, D.L. / Xavier, A.V.
#2: Journal: Inorg.Chim.Acta. / Year: 1998
Title: Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 A Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 A Resolution
Authors: Simoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A.
#3: Journal: Biochemistry / Year: 1995
Title: Structure of the Tetraheme Cytochrome from Desulfovibrio Desulfuricans Atcc 27774: X-Ray Diffraction and Electron Paramagnetic Resonance Studies
Authors: Morais, J. / Palma, P.N. / Frazao, C. / Caldeira, J. / Legall, J. / Moura, I. / Moura, J.J. / Carrondo, M.A.
History
DepositionSep 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2004Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0925
Polymers11,6181
Non-polymers2,4744
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.680, 61.680, 106.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

21A-2032-

HOH

31A-2122-

HOH

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Components

#1: Protein CYTOCHROME C3 / CYTC3


Mass: 11618.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q9L915
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.2 %
Crystal growpH: 7.6 / Details: pH 7.60

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DIMOND (III) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 44219 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.32 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.4→1.43 Å / Rmerge(I) obs: 0.279 / % possible all: 98.5

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Processing

Software
NameClassification
SHELXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.4→30 Å / Num. parameters: 10377 / Num. restraintsaints: 13386 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 1210 5.3 %RANDOM
all0.1469 22816 --
obs0.1472 -94.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1104.05
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 172 147 1127
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0.011
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.071

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